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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000002,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000995,UBERON:0001062,UBERON:0001560,UBERON:0002050,UBERON:0002532,UBERON:0003100,UBERON:0003133,UBERON:0003134,UBERON:0003975,UBERON:0004120,UBERON:0004175,UBERON:0005156,UBERON:0005423,UBERON:0005795
|ancestors_in_anatomy_facet=UBERON:0000002,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000995,UBERON:0001062,UBERON:0001560,UBERON:0002050,UBERON:0002532,UBERON:0003100,UBERON:0003133,UBERON:0003134,UBERON:0003975,UBERON:0004120,UBERON:0004175,UBERON:0005156,UBERON:0005423,UBERON:0005795
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120,FF:0101967
|fonse_cell_line=FF:0101120,FF:0101967
|fonse_cell_line_closure=FF:0101120,FF:0101967
|fonse_cell_line_closure=FF:0101120,FF:0101967

Revision as of 16:32, 29 March 2012


Name:epidermoid carcinoma cell line:Ca Ski
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecervix
dev stage40 year old adult
sexfemale
age40
cell typeunclassifiable
cell lineCa Ski
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.038
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.642
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10748

Jaspar motifP-value
MA0002.20.0168
MA0003.10.0904
MA0004.10.267
MA0006.10.944
MA0007.10.318
MA0009.10.353
MA0014.10.0384
MA0017.10.0738
MA0018.20.102
MA0019.10.73
MA0024.11.29996e-5
MA0025.10.597
MA0027.10.656
MA0028.10.0243
MA0029.10.15
MA0030.10.831
MA0031.10.913
MA0035.20.0898
MA0038.16.84961e-4
MA0039.20.00177
MA0040.10.0484
MA0041.10.291
MA0042.10.111
MA0043.10.162
MA0046.10.674
MA0047.20.483
MA0048.10.128
MA0050.10.695
MA0051.10.828
MA0052.10.917
MA0055.13.93476e-4
MA0057.10.598
MA0058.10.45
MA0059.10.382
MA0060.14.85558e-13
MA0061.10.111
MA0062.20.0122
MA0065.20.35
MA0066.10.197
MA0067.10.887
MA0068.10.23
MA0069.10.681
MA0070.10.453
MA0071.10.21
MA0072.10.908
MA0073.10.764
MA0074.10.422
MA0076.10.041
MA0077.10.221
MA0078.10.622
MA0079.20.605
MA0080.20.0106
MA0081.10.657
MA0083.10.96
MA0084.10.386
MA0087.10.253
MA0088.10.911
MA0090.10.00225
MA0091.10.00425
MA0092.10.213
MA0093.10.279
MA0099.25.95473e-14
MA0100.10.41
MA0101.10.893
MA0102.20.91
MA0103.10.00298
MA0104.20.0164
MA0105.17.68307e-4
MA0106.18.08062e-4
MA0107.10.742
MA0108.20.0297
MA0111.10.821
MA0112.20.00101
MA0113.10.0336
MA0114.10.536
MA0115.10.688
MA0116.10.00701
MA0117.10.881
MA0119.10.458
MA0122.10.842
MA0124.10.173
MA0125.10.0902
MA0131.10.271
MA0135.10.586
MA0136.10.767
MA0137.20.934
MA0138.20.00139
MA0139.10.584
MA0140.10.155
MA0141.10.0808
MA0142.10.792
MA0143.10.37
MA0144.10.984
MA0145.10.176
MA0146.10.559
MA0147.10.0294
MA0148.10.633
MA0149.10.17
MA0150.10.171
MA0152.10.282
MA0153.10.81
MA0154.10.0408
MA0155.10.121
MA0156.10.224
MA0157.10.729
MA0159.10.818
MA0160.10.7
MA0162.10.686
MA0163.10.0162
MA0164.10.849
MA0258.10.00385
MA0259.10.0713



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10748

Novel motifP-value
10.233
100.615
1000.383
1010.0888
1020.458
1030.402
1040.867
1050.701
1060.0233
1070.411
1080.99
1090.367
110.0974
1100.922
1110.831
1120.058
1130.257
1140.0771
1150.0669
1160.135
1170.884
1180.534
1190.123
120.802
1200.997
1210.516
1220.256
1230.355
1240.0417
1250.0852
1260.777
1270.802
1284.90598e-4
1290.892
130.181
1300.0521
1310.27
1320.74
1330.317
1340.06
1350.00931
1360.0336
1370.0966
1380.867
1390.0296
140.428
1400.554
1410.808
1420.633
1430.151
1440.0369
1450.588
1460.689
1470.683
1480.264
1490.0302
150.479
1500.959
1510.446
1520.475
1530.996
1540.654
1550.681
1560.47
1570.716
1580.482
1590.921
160.569
1600.5
1610.225
1620.758
1630.654
1640.806
1650.497
1660.296
1670.701
1680.666
1690.128
170.774
180.126
190.0247
20.62
200.104
210.634
220.181
230.172
240.267
250.953
260.68
270.081
280.636
290.577
30.23
300.753
310.0825
320.00985
330.196
340.168
350.02
360.676
370.24
380.703
390.852
40.722
400.166
410.382
420.604
430.0912
440.0978
450.736
460.113
470.413
480.54
490.15
50.0677
500.351
510.325
520.529
530.503
540.208
550.131
560.599
570.869
580.62
590.0949
60.408
600.281
610.548
620.241
630.795
640.661
650.042
660.00264
670.586
680.174
690.594
70.711
700.0169
710.456
720.276
730.488
740.0853
750.734
760.815
770.263
780.156
790.00215
80.165
800.298
810.0526
821.2444e-4
830.688
840.741
850.00118
860.405
870.117
880.908
890.116
90.147
900.103
910.0745
920.0428
930.413
940.123
950.113
960.0458
970.756
980.142
990.895



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs10748


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
1749 (squamous cell carcinoma)
305 (carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000002 (uterine cervix)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000995 (uterus)
0001062 (anatomical entity)
0001560 (neck of organ)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0003975 (internal female genitalia)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005795 (embryonic uterus)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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